recipe bioconductor-epivizr

R Interface to epiviz web app

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/epivizr.html

License:

Artistic-2.0

Recipe:

/bioconductor-epivizr/meta.yaml

Links:

biotools: epivizr, doi: 10.1038/nmeth.3038

This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.

package bioconductor-epivizr

versions:

2.32.0-0,  2.30.0-0,  2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0, 

2.32.0-0,  2.30.0-0,  2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.12.0-0,  2.10.0-0,  2.8.0-0

depends bioconductor-bumphunter:

>=1.44.0,<1.45.0

depends bioconductor-epivizrdata:

>=1.30.0,<1.31.0

depends bioconductor-epivizrserver:

>=1.30.0,<1.31.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-epivizr

and update with::

   mamba update bioconductor-epivizr

To create a new environment, run:

mamba create --name myenvname bioconductor-epivizr

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-epivizr:<tag>

(see `bioconductor-epivizr/tags`_ for valid values for ``<tag>``)

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-epivizr/README.html)